Package org.biojava3.genome.parsers.gff
Class LocIterator
java.lang.Object
org.biojava3.genome.parsers.gff.LocIterator
Move a sliding window over a Location. Window size and increment can be specified. If the
increment is negative, the iteration starts at end of Location and moves toward beginning.
- Author:
- Hanno Hinsch
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Constructor Summary
ConstructorDescriptionLocIterator
(Location bounds, int windowSize, int increment) Construct an iterator that slides a window over a Location. -
Method Summary
Modifier and TypeMethodDescriptionboolean
hasNext()
Check if next window of default size is available.boolean
hasNext
(int windowSize, int increment) Check if next window of specified size is available.static void
Deprecated.next()
Get next window of default size, then increment position by default amount.next
(int windowSize, int increment) Get next window of specified size, then increment position by specified amount.Get portion of bounding location that has not yet been retrieved by next() method.void
remove()
Unsupported.toString()
Get string representation of iterator.Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Details
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LocIterator
Construct an iterator that slides a window over a Location.- Parameters:
bounds
- The location over which to iterate.windowSize
- The size of the moving window.increment
- The increment by which to move the window at each iteration. If increment is positive, the iteration starts at the beginning of the bounding location and moves toward the end; if the increment is negative, the iteration starts at the end and moves toward the begnning.
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Method Details
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hasNext
public boolean hasNext(int windowSize, int increment) Check if next window of specified size is available.- Parameters:
windowSize
- Size of window. May be smaller or larger than default window size.increment
- The increment by which to move the window at each iteration. Note that this method does not actually change the position. However, it checks the sign of the increment parameter to determine the direction of the iteration.- Returns:
- True if window of specified size is available.
- Throws:
IllegalArgumentException
- Window size parameter was not positive.
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hasNext
public boolean hasNext()Check if next window of default size is available. -
remainder
Get portion of bounding location that has not yet been retrieved by next() method.- Returns:
- The location not yet retrieved.
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next
Get next window of default size, then increment position by default amount. Both defaults are specified in the LocIterator constructor.- Specified by:
next
in interfaceIterator<Location>
- Returns:
- Location of next window.
- Throws:
IndexOutOfBoundsException
- The next window was not within the bounding location.
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next
Get next window of specified size, then increment position by specified amount.- Parameters:
windowSize
- Size of window to get.increment
- Amount by which to shift position. If increment is positive, the position is shifted toward the end of the bounding location; if increment is negative, the position is shifted toward the beginning of the bounding location.- Returns:
- Location of next window.
- Throws:
IndexOutOfBoundsException
- The next window was not within the bounding location.IllegalArgumentException
- The increment was zero, or windowSize was not positive.
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toString
Get string representation of iterator. -
remove
public void remove()Unsupported.- Specified by:
remove
in interfaceIterator<Location>
- Throws:
UnsupportedOperationException
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main
Deprecated.
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